Paleontology reveals that all natural diets also had heart disease. Suck it paleo dieters!
There are risk factors for arteriosclerosis other than a fatty diet, like alcohol abuse and/or smoking. If you drink enough alcohol, you can end up with a liver that's overtaxed processing that, and can't get to the fat, so you get fat building up in your blood.
From the study page, linked at the bottom of the article,
Individuals from ancient Egypt, ancient Peru, the Ancestral Puebloans of southwest America, and the Unangan of the Aleutian Islands were imaged.
The Egyptians definitely had beer, and likely the puebloans too.
Dunno about the other populations, but you can end up with a high level of fat in your blood via a few different roads. This paragraph
from the heart research institute says it pretty well.
Risk factors for atherosclerosis
90 per cent of Australians have one modifiable risk factor for heart disease. The major modifiable risk factors include smoking, high blood pressure, high blood cholesterol, insufficient physical activity, obesity, diabetes, poor nutrition, and excessive intake of alcohol. Other risk factors that are beyond our control include age, gender, family history and ethnicity.
Hunter gatherers didn't have great nutrition (usually having a month or more a year where food was very scarce), booze was present in a lot of ancient cultures etc. Just because they didn't experience the exact causal process that we have, doesn't mean that the causal process identified to effect millions of people doesn't exist.